Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of Metazoa, and consequences for phylogenetic inferences
Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of Metazoa, and consequences for phylogenetic inferences
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DOI：
10.1080/10635150590947843
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发表时间：
2005-04-01
影响因子：
6.5
通讯作者：
Deutsch, J
中科院分区：
文献类型：
--
作者：
Hassanin, A;Léger, N;Deutsch, J
线粒体DNA（mtDNA）序列通常用于推断系统发育关系。然而，链特定的偏好，在核苷酸组成的mtDNA，这被认为是反映不对称突变的限制，结合重要的组成异质性类群之间，是已知的系统发育分析的高度问题。在这里，比较了49种后生动物（34种节肢动物，2种环节动物，2种软体动物和11种后体动物）的核苷酸组成，并分析了包括6个蛋白质编码基因的mtDNA片段，即，ATP 6、ATP 8、COX 1、COX 2、COX 3和NAD 2。分析表明，大多数后生动物物种呈现出明显的链不对称性，其中一条链偏向A和C，而另一条链具有反向偏向，即，支持T和G这种链偏好的起源可能与不对称突变限制有关，涉及复制和/或转录过程中A和C核苷酸的脱氨基。分析表明，六个不相关的属的特征是通常的链偏置的逆转，即，Argiope（蜘蛛目）、Euscorpius（蝎子目）、Tigriopus（颚足目）、Branchiostoma（脊索动物）、Florometra（棘皮动物）和Katharina（软体动物）。有人提出，不对称突变的限制已被独立逆转，在这六个属，通过反转的控制区，即，含有大多数线粒体DNA复制和转录调节元件的区域。我们发现，逆转的不对称突变的限制有显着的后果的系统发育分析，分类群的特点是反向链偏见往往组在一起，由于长分支吸引文物。我们提出了一种新的方法，限制这个特定的问题，在树重建贝叶斯方法。我们应用我们的方法来处理节肢动物的主要谱系的系统发育关系的问题。这种新方法提供了一个更好的一致性与核分析的基础上18 S rRNA基因序列。与以往基于线粒体DNA序列的研究结果相比，我们的数据表明，螯肢类、甲壳类、多足类、泛甲壳类和副足类是单系的。
Mitochondrial DNA ( mtDNA) sequences are commonly used for inferring phylogenetic relationships. However, the strand-specific bias in the nucleotide composition of the mtDNA, which is thought to reflect asymmetric mutational constraints, combined with the important compositional heterogeneity among taxa, are known to be highly problematic for phylogenetic analyses. Here, nucleotide composition was compared across 49 species of Metazoa ( 34 arthropods, 2 annelids, 2 molluscs, and 11 deuterosomes), and analyzed for a mtDNA fragment including six protein-coding genes, i.e., atp6, atp8, cox1, cox2, cox3, and nad2. The analyses show that most metazoan species present a clear strand asymmetry, where one strand is biased in favor of A and C, whereas the other strand has a reverse bias, i.e., in favor of T and G. The origin of this strand bias can be related to asymmetric mutational constraints involving deaminations of A and C nucleotides during the replication and/or transcription processes. The analyses reveal that six unrelated genera are characterized by a reversal of the usual strand bias, i.e., Argiope (Araneae), Euscorpius (Scorpiones), Tigriopus (Maxillopoda), Branchiostoma (Cephalochordata), Florometra ( Echinodermata), and Katharina ( Mollusca). It is proposed that asymmetric mutational constraints have been independently reversed in these six genera, through an inversion of the control region, i.e., the region that contains most regulatory elements for replication and transcription of the mtDNA. We show that reversals of asymmetric mutational constraints have dramatic consequences on the phylogenetic analyses, as taxa characterized by reverse strand bias tend to group together due to long-branch attraction artifacts. We propose a new method for limiting this specific problem in tree reconstruction under the Bayesian approach. We apply our method to deal with the question of phylogenetic relationships of the major lineages of Arthropoda. This new approach provides a better congruence with nuclear analyses based on 18S rRNA gene sequences. By contrast with some previous studies based on mtDNA sequences, our data suggest that Chelicerata, Crustacea, Myriapoda, Pancrustacea, and Paradoxopoda are monophyletic.